By ship
SuperFerry (http://www.superferry.com.ph/) and Negros Navigation (http://www.negrosnavigati...) both have a weekly ferry to Puerto Princesa from Manila. The ferry trip is about 22 hours long.
Milagrosa Shipping has a weekly ferry that sails between Puerto Princesa - Cuyo Islands - Iloilo. It departs Iloilo at 7pm on Thursday, arrives at the Cuyo Islands at 8am Friday, departs Cuyo Islands 3pm Friday and arrives in Puerto Princesa at 8am on Saturday.
By plane
Puerto Princesa is slightly more than an hour away by plane from Manila. Philippine Airlines (http://www.philippineairl...), Cebu Pacific (http://www.cebupacificair.com/) and Air Philippines (http://www.airphils.com/), Zest Air (http://www.zestair.com.ph/) all have daily flights from Manila to Puerto Princesa. Air Philippines and Cebu Pacific also operates flights to and from Puerto Princesa to other major cities such as Davao and Cebu City. SEAIR (http://flyseair.com/) offers flights from Busuanga Tu/F/Su and El Nido on Tu/F.Starting from this year 2012, there are now daily connecting/return budget flights by Philippines AirAsia from Clark/Angeles City in Luzon direct to Puerto Princesa.
The airport is practically in the city centre so you can ignore the overpriced tricycles waiting in front of the arrival and catch a tricycle on the main road for a fare of 7-10 pesos per passenger.
The airport is small and can be closed at certain points in the day e.g. between 2pm and 3pm and there are only 2 cafes and some local eateries outside the airport, therefore don't plan to kill any time here.